Nucleic Acid Databases (NDB ) of bioinformatics pptx

Nucleic Acid Database

1. Nucleic Acid Database Presented by – Karmandeep kaur M. Sc. 1 st Sem ( Biotechnology )

2. NUCLEIC ACID DATABASE

3. Synopsis Biological Databases Types of Biological Databases Nucleic Acid Databases Types of Nucleic acids Database Primary Databases GenBank EMBL DDBJ INSDC Applications

4. Biological Databases Biological databases are digital repositories of biological data, such as DNA sequences, protein sequences, protein structures, and gene expression data. They are used by scientists to store, organize, and analyze biological data to advance our understanding of life. Biological databases are essential for biological research. They provide scientists with a wealth of data to mine for insights into the molecular basis of life.

5. Nucleic Acid Databases A nucleotide database is a comprehensive repository of genetic information that is designed to store and organize nucleotide sequences that are derived from both DNA and RNA molecules. The Nucleotide database is a collection of sequences from several sources, including GenBank, RefSeq, TPA and PDB. The Nucleic Acid Database (NDB) (Berman et al., 1992) was established in 1991 as a resource for specialists in the field of nucleic acid structure. It is a centralized platform for storing and accessing structural information and annotations related to nucleic acids.

6. Types of Nucleic acids Database

7. Primary Databases Primary databases  are populated with experimentally derived data such as nucleotide sequence, protein sequence or macromolecular structure. Experimental results are submitted directly into the database by researchers, and the data are essentially archival in nature. Once given a database accession number, the data in primary databases are never changed: they form part of the scientific record.

8. GenBank The  GenBank  sequence database is an open access, annotated collection of all publicly available nucleotide sequences and their protein translations. This database is produced at the National Center for Biotechnology Information (NCBI) as part of the International Nucleotide Sequence Database Collaboration (INSDC). The NCBI is located in Bethesda, Maryland, and was founded in 1988 through legislation sponsored by US Congressman Claude Pepper.  GenBank and its collaborators receive sequences produced in laboratories throughout the world from more than 100,000 distinct organisms. GenBank continues to grow at an exponential rate, doubling every 18 months. GenBank is built by direct submissions from individual laboratories, as well as from bulk submissions from large-scale sequencing centers, and submissions from private individuals.

9. EMBL EMBL’s European Bioinformatics Institute (EMBL- EBI), founded in 1994, provides freely available data, bioinformatics services and training to the life science community worldwide.   EMBL-EBI is part of the , an intergov European Molecular Biology Laboratory (EMBL) , an intergovernmental research organisation funded by over 20 member states, prospect and associate member states. EMBL-EBI’s co-location with the Wellcome Sanger Institute offers vital synergies. EMBL-EBI maintains the world’s most comprehensive range of molecular data resources, developed in collaboration with colleagues worldwide, and open to all.  EMBL is also actively engaged in developing its discoveries to benefit society. EMBL’s technology transfer partner,  EMBLEM , identifies, protects, and commercialises the intellectual property developed at EMBL, as well as by EMBL alumni and third parties.

10. DDBJ The DNA Data Bank of Japan is a public database of nucleotide sequences established at the National Institute of Genetics (NIG). Since 1987, the DDBJ has been collecting annotated nucleotide sequences as its traditional database service. The principal purpose of DDBJ operations is to improve the quality of INSD, as public domains. When researchers make their data open to the public through INSD and commonly shared in worldwide, we at DDBJ Center make efforts to describe information on the data as rich as possible, according to the unified rules of INSD, preferably without any stress by using DDBJ. DDBJ serves as the only nucleotide sequence archive database in Asia. 

11. INSDC The International Nucleotide Sequence Database Collaboration (INSDC) is a long-standing foundational initiative that operates between  DDBJ ,  EMBL-EBI  and  NCBI . INSDC covers the spectrum of data raw reads, through alignments and assemblies to functional annotation, enriched with contextual information relating to samples and experimental configurations. The INSDC members work together to ensure that all public domain nucleotide sequence data deposited in the archives is preserved as part of the scientific record and is accessible in standardized formats across the three sites through daily data exchange.

12. Application of Nucleic Acid Database Nucleotide databases are used to identify the gene or the function of a particular nucleotide sequence by comparing an unknown sequence with the known sequences in the database. Nucleotide databases can be used to study and examine gene expression by using the sequence information stored in the databases. Nucleotide databases are also used to identify potential drug targets and develop new therapies for genetic diseases. Nucleotide databases also help in identifying genetic variations that may be linked to diseases, which ultimately helps in the development of diagnostic tools and treatments. Nucleotide databases can be used in phylogenetic analysis to analyze the evolutionary relationships between organisms, by comparing and examining their DNA or RNA sequences.

13. References https://www.ncbi.nlm.nih.gov/nucleotide/#:~:text=The%20Nucleotide%20database%20is%20a,for%20biomedical%20research%20and%20discovery. https://www.linkedin.com/pulse/biological-database-stephen-rufushttps://www.linkedin.com/pulse/biological-database-stephen-rufushttps://onlinelibrary.wiley.com/iucr/itc/Fa/ch24o2v0001/ch24o2.pdf https://www.ebi.ac.uk/training/online/courses/bioinformatics-terrified/what-makes-a-good-bioinformatics-database/primary-and-secondary-databases/ https://isogg.org/wiki/GenBank https://www.wellcomegenomecampus.org/aboutus/embl-ebi/ https://www.ddbj.nig.ac.jp/about/index-e.html https://www.insdc.org/